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Threads Started By: markber
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Why Science is broken (and how to fix it)
An interesting post from a blog that BioNMR does not aggregate:
Why Science is broken (and how to fix it)
By Morgan Giddings
1 September 2011
Bell Labs was a remarkable enterprise which, according to Wikipedia, contributed to the development of cell phones, wlan (wifi), semiconductors, compression algorithms, and many more developments that changed the way people interact with technology.
Bell Labs worked well because they brought together innovative thinkers, and let them innovate. People there didn’t have to write grant proposals, teach students, serve on committees, or work on...
markber
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markber
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NMR software feature requests |
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markber
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The BMRB matters
The BMRB matters
Nature Structural & Molecular Biology 19, 853 (2012) doi:10.1038/nsmb.2387
Published online 06 September 2012
NATURE STRUCTURAL & MOLECULAR BIOLOGY | EDITORIAL
http://www.nature.com/nsmb/journal/v19/n9/full/nsmb.2387.html
markber
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TWO FACULTY POSITIONS in MOLECULAR STRUCTURE & FUNCTION THE HOSPITAL FOR SICK CHILDREN, TORONTO, ON, CANADA
TWO FACULTY POSITIONS in MOLECULAR STRUCTURE & FUNCTION
THE HOSPITAL FOR SICK CHILDREN, TORONTO, ON, CANADA
To coincide with the opening of The Hospital for Sick Children’s (SickKids) new
Centre for Research and Learning in August 2013, the Program in Molecular
Structure & Function (MSF) is seeking two exceptional individuals who are
interested in exploiting the unique research environment provided by Canada’s
largest paediatric hospital-based research institute (Sickkids - hospital
Research/AbouttheInstitute/index.html). Individuals, at all stages of their career,
that use...
markber
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Job marketplace |
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markber
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9,537 |
NMR presentations |
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Three-days HADDOCK workshop in Vilnius
LINK
Description
HADDOCK is an information-driven docking program developed at Utrecht University, which is widely used in the structural biology community and has demonstrated a strong performance in the blind docking competition CAPRI.
The workshop will be given by Prof. Alexandre Bonvin with a number of his group members. It will consist of lectures in the morning and hands-on sessions on computers in the afternoon.
Sign ups are limited to 20 people. For these, experience with Linux is a requisite. The workshop will cover various aspects of the modelling of biomolecular...
markber
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GeNMR - template-based structure generation from NMR data
GeNMR website
GeNMR (GEnerate NMR structures) is a web server for template-based or ab initio generation of 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. The web server produces an ensemble of PDB coordinates within a period ranging from 20 minutes to 4 hours, depending on protein size, server load, quality and type of experimental information, and selected protocol options.
References:
1. Berjanskii M, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS. (2009)GeNMR: a web server for rapid NMR-based...
markber
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CS23D - generating protein structure from NMR chemical shifts and sequence homology
CS23D website
CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. CS23D uses a combination of maximal subfragment assembly, chemical shift threading, shift-based torsion angle prediction and chemical shift refinement to generate and refine the protein coordinates. CS23D accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein normally within 10-15 minutes (3 hours max). CS23D performance is dependent on the completeness of the chemical shift assignments and...
markber
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RCI - Random Coil Index for predicting protein flexibility from chemical shifts
RCI website
RCI method predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts and predicting values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.
The key advantages of this protocol over existing methods of studying protein flexibility are (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone...
markber
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NMR software |
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Protein NMR - A Practical Guide - Solid-state MAS NMR Spectra
Below is a Google-cached version of Protein NMR - A Practical Guide - Solid-state MAS NMR Spectra
page from www.protein-nmr.org.uk crashed on 11/6/11. You may want to check first if the site has been restored since it would also display images or/and have a more updated info.
Spectrum Descriptions
This page contains a list of some solid-state magic-angle spinning (MAS) NMR experiments which are useful for protein solid-state MAS NMR assignment and structure calculations. For each experiment there is short description and an illustration showing the observed magnetisation...
markber
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Cashed version of protein-nmr.org.uk |
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Protein NMR - A Practical Guide - Solution NMR Assignment - Practice
Below is a Google-cached version of Protein NMR - A Practical Guide - Solution NMR Assignment - Practice page from www.protein-nmr.org.uk that went down on 11/6/11. You may want to check first if the site has been restored since it would also display images or/and have a more updated info.
Assignment - Practice (for Analysis 2.1)
This section describes how the assignment principles described under Assignment - Theory can be but put into practice using the CCCPNmr Analysis software. There are several ways in which triple resonance backbone assignment, in particular, can be approached...
markber
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Cashed version of protein-nmr.org.uk |
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Protein NMR - A Practical Guide - Glossary / Abbreviations
Below is a Google-cached version of Protein NMR - A Practical Guide - Glossary / Abbreviations page from www.protein-nmr.org.uk crashed on 11/6/11. You may want to check first if the site has been restored since it would also display images or/and have a more updated info.
Glossary and Abbreviations
2D
two-dimensional
3D
three-dimensional
Double Labelled
markber
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Cashed version of protein-nmr.org.uk |
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Protein NMR - A Practical Guide - Solution NMR Assignment Theory
Below is a Google-cached version of Protein NMR - A Practical Guide - Solution NMR Assignment Theory page from www.protein-nmr.org.uk crashed on 11/6/11. You may want to check first if the site has been restored.
Assignment - Theory
The most simple and straight forward method of backbone resonance assignment involves the use of 15N,13C labelled protein and the measurement of CBCANNH and CBCA(CO)NNH spectra.
Large Proteins
Large proteins give worse NMR spectra, because they tumble more slowly. For this reason the CBCANNH and CBCA(CO)NNH spectra of larger proteins (> 150...
markber
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Cashed version of protein-nmr.org.uk |
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Protein NMR - A Practical Guide - Solution NMR Spectra
Below is a Google-cached version of Protein NMR - A Practical Guide - Solution NMR Spectra page from www.protein-nmr.org.uk crashed on 11/6/11. You may want to check first if the site has been restored.
Spectrum Descriptions
This page contains a list of the solution NMR experiments most commonly used in protein NMR assignment and structure calculation. For each experiment there is an illustration showing which atoms are observed (pink) and through which atoms magnetisation flows (light blue). An example spectrum shows what it should look like and particular features and...
markber
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Cashed version of protein-nmr.org.uk |
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Protein NMR - A Practical Guide
Below is a Google-cached version of Protein NMR - A Practical Guide page from crashed protein-nmr.org.uk. You may want to check first if the site was restored.
Most books on Protein NMR focus on theoretical aspects and pulse sequences with only little space devoted to resonance assignment and structure calculations. At the same time many software manuals provide detailed information on how to use the software, but assume prior knowledge of the concepts of assignment and structure calculation. This has produced a gap in this area which these webpages aim to bridge by describing the ...
markber
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Keystone Symposia Frontiers of NMR in Biology 2011
<table><tbody><tr><td align="center">Organizers: Michael F. Summers, Dorothee Kern and David E. Wemmer
January 8 - 13, 2011 • Big Sky Resort • Big Sky, Montana </td><td align="center">
</td></tr></tbody></table>
Conference website
Meeting Summary
Nuclear magnetic resonance (NMR) spectroscopy is now a well-established tool for determining structures of small to moderate size biomacromolecules. The horizon is expanding, however, through recent methodological advances, including the evolution of approaches...
markber
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markber
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Prof. Konstantin Pervushin's NMR group
Prof. Konstantin Pervushin affiliation:
Structural Biology
Biozentrum, University of Basel
Basel / Switzerland
http://www.biozentrum.unibas.ch/associated_group/pervushin/images/konstantinB.jpg
A copy of Porf. Pervushin's research interests from the group website:
markber
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Michael Gryk's NMR group, University of Connecticut, USA
Below is a copy of information about Gryk's lab from the website of University of Connecticut.
<table width="100%" border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="padding: 10px 20px 20px;" valign="top" width="45%" align="left">Michael R. Gryk
Associate Professor of Molecular, Microbial and Structural Biology
gryk@uchc.edu
B.S., M.S., University of Connecticut
markber
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CONNJUR - open source integration environment for biomolecular NMR data analysis
CONNJUR Project website
The CONNJUR Project is developing an open source integration environment for biomolecular NMR data analysis. CONNJUR software is a workflow generator, based on legacy NMR analysis applications, that is being developed as Open Source Software -- it is perpetually free for anyone to use, modify and distribute.
CONNJUR is developed by a community of NMR spectroscopists and scientific programmers who aim to create and maintain NMR analysis tools bounded by the goals of excellent end-product, free of charge, open source software using the...
markber
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NMR Postdoctoral Associate - Steve M. King group - University of Connecticut
An NIH-funded postdoctoral position is available immediately in the laboratory of Dr. Steve M. King in the Department of Biochemistry. The project involves determination of the structure and dynamics of components of the dynein microtubule motor complex using NMR spectroscopy. A strong background in biophysics is required. Applications should be sent by email to steve@king2.uchc.edu.
source: structbio.uchc.edu/positions.html
markber
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NMR postdoctoral positions - Alexandrescu's Group - University of Connecticut
Several postdoctoral positions are available in the laboratory of Dr Andrei Alexandrescu at the UConn-Storrs campus. The aim of this NSF-funded project is to obtain an improved structural description of protein folding. A particular area of emphasis is to explore the use of NMR residual dipolar couplings data for the structural characterization of non-native states. A related interest is the development of methods for increasing the efficiency of NMR structure determination by combining "knowledge-based" restraints with the smallest possible number of experimentally-derived NMR restraints....
markber
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Postdoctoral position in NMR software development - University of Connecticut Health
Positions Opening
Programmer: We are looking for an enthusiastic and energetic individual to continue development of the CONNJUR framework. Knowledge and experience with object-oriented programming and the JAVA programming language required. Familiarity with UNIX and shell programming would be a plus.
Post-doctoral Associate: We are looking for a knowledgeable NMR researcher to expand the working scope of the CONNJUR application. Knowledge of the NMR processing pipeline and hands-on experience using NMR to solve biological problems is expected of the candidate. An...
markber
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Post Doctoral Fellow NMR position in the lab of Damodaran Krishnan
Contact Name: Damodaran Krishnan
Contact Email: damodak@pitt.edu
Contact Telephone: 412-624-8403
Employer: University of Pittsburgh
Background
A post doctoral position is available at the chemistry department at University of Pittsburgh to study the interaction of CO2 with Ionic liquids and other sorbents using high resolution NMR spectroscopy. The facility is fully equipped with state-of-the-art Bruker Avance III NMR spectrometers, including 300, 400, 500, 600 and 700 MHz spectrometers. The post-doctoral...
markber
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